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Table 5 COSMIC mutation analysis by considering genes related to PPIs predicted from best methods in our and PERA approaches and the relative amount of somatic and germline mutated genes

From: INBIA: a boosting methodology for proteomic network inference

Cancer type Somatic mutation Germline mutation
BLCA ERBB3,NOTCH1,TSC1
BRCA AKT1,ARID1A,BAP1,BRCA2,CCND1,CDH1,CDKN1B,  
  ERBB2,ESR1,NOTCH1,PIK3CA,RB1,TP53 BRCA2,CHEK2,RB1,TP53
  AKT1,BRCA2,CCND1,CDH1,CDKN1B,ERBB2,ESR1, BRCA2,CHEK2,TP53
  GATA3,NOTCH1,PIK3CA,TP53  
COAD ERBB3
GBM PIK3CA,PIK3R1
HNSC ERBB3,MTOR,NOTCH1,TSC2
KIRC MET,MTOR,NF2,TSC1,TSC2,VHL MET,TSC1,TSC2,VHL
  MET,MTOR,TSC1,TSC2,VHL  
LGG BRAF,EGFR,PTEN,RAF1,TP53 ATM,PTEN,TP53
LUAD NOTCH1,RB1,TP53 RB1
 
LUSC NOTCH1,RB1,TP53 RB1
  TP53
OV AKT1,ARID1A,BRAF,BRCA2,CCNE1,CTNNB1,ERBB2, BRCA2,MSH2,MSH6,STK11
  MAPK1,MSH2,PIK3R1  
  AKT1,BRAF,CCNE1,CTNNB1,ERBB2,MAPK1,PIK3R1
PRAD AR,BRAF,NDRG1,PTEN,RAF1 PTEN
  AR,BRAF,RAF1
READ AKT1,BRAF,CTNNB1,MAP2K1,MSH2,MSH6,PIK3CA, MSH2,MSH6
  PIK3R1,SMAD3,SMAD4,SRC,TP53  
  AKT1,BRAF,CTNNB1,MAP2K1,PIK3CA,PIK3R1,SMAD3,SMAD4,SRC,TP53
SKCM ERBB3,NOTCH1
STAD BRAF,CDH1,ERBB2,ERBB3,PIK3CA CDH1
THCA BRAF,MTOR CDKN1B
  BRAF,NRAS  
UCEC MSH2,MTOR,PTEN,SRC MSH2,MSH6,PTEN
  MTOR,PTEN,SRC,YWHAE PTEN
  1. For each cancer type, tuple highlighted in italic refers to our method (INBIA), the second one to PERA. When only one record per cancer type is present then it means that the two approaches achieved the same results